Xenopus embryos divide rapidly following fertilization. During this rapid period of cleavage, cell divisions are not sensitive to DNA replication or spindle assembly inhibition. Here, we have investigated the consequences of eliciting DNA damage in these embryos. We show that the rapid cell divisions are not affected by DNA damage. However, as the embryos reach the onset of gastrulation, they undergo rapid and synchronous apoptosis. We have investigated the regulation on this delayed apoptotic response to DNA damage. Next, we have reconstituted a DNA damage cell cycle checkpoint in vitro, demonstrating that all the checkpoint signalling components are present in the embryos but are not activated under the experimental conditions used to generate DNA damage in the embryo.